Human ptp1b complexed with tpicooh

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural basis for inhibition of the protein tyrosine phosphatase 1B by phosphotyrosine peptide mimetics.

Groves, M.R.Yao, Z.-J.Roller, P.P.Burke Jr., T.R.Barford, D.

(1998) Biochemistry 37: 17773-17783

  • DOI: https://doi.org/10.1021/bi9816958
  • Primary Citation of Related Structures:  
    1BZC, 1BZH, 1BZJ

  • PubMed Abstract: 

    Protein tyrosine phosphatases regulate diverse cellular processes and represent important targets for therapeutic intervention in a number of diseases. The crystal structures of protein tyrosine phosphatase 1B (PTP1B) in complex with small molecule inhibitors based upon two classes of phosphotyrosine mimetics, the (difluoronaphthylmethyl)phosphonic acids and the fluoromalonyl tyrosines, have been determined to resolutions greater than 2.3 A. The fluoromalonyl tyrosine residue was incorporated within a cyclic hexapeptide modeled on an autophosphorylation site of the epidermal growth factor receptor. The structure of this inhibitor bound to PTP1B represents the first crystal structure of a non-phosphonate-containing inhibitor and reveals the mechanism of phosphotyrosine mimicry by the fluoromalonyl tyrosine residue and the nature of its interactions within the catalytic site of PTP1B. In contrast to complexes of PTP1B with phosphotyrosine-containing peptides, binding of the fluoromalonyl tyrosine residue to the catalytic site of PTP1B is not accompanied by closure of the catalytic site WPD loop. Structures of PTP1B in complex with the (difluoronaphthylmethyl)phosphonic acid derivatives reveal that substitutions of the naphthalene ring modulate the mode of inhibitor binding to the catalytic site and provide the potential for enhanced inhibitor affinity and the generation of PTP-specific inhibitors. These results provide a framework for the rational design of higher affinity and more specific phosphotyrosine mimetic inhibitors of not only protein tyrosine phosphatases but also SH2 and PTB domains.

  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gene Names: PTPN1PTP1B
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
PHAROS:  P18031
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18031
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PIC

Download Ideal Coordinates CCD File 
C12 H9 F2 O5 P
Binding Affinity Annotations 
IDSourceBinding Affinity
PIC Binding MOAD:  1BZJ Ki: 2.20e+4 (nM) from 1 assay(s)
PDBBind:  1BZJ Ki: 2.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.45α = 90
b = 88.45β = 90
c = 104.88γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description